3DH3

Crystal Structure of RluF in complex with a 22 nucleotide RNA substrate

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF01479	e3dh3A2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Alpha-L RNA-binding motif	F: PF01479	ECOD (1.6)
A	PF00849	e3dh3A1	A: a+b two layers	X: Alpha-beta plaits	H: Pseudouridine synthase (From Topology)	T: Pseudouridine synthase	F: PF00849	ECOD (1.6)
C [auth B]	PF01479	e3dh3B2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Alpha-L RNA-binding motif	F: PF01479	ECOD (1.6)
C [auth B]	PF00849	e3dh3B1	A: a+b two layers	X: Alpha-beta plaits	H: Pseudouridine synthase (From Topology)	T: Pseudouridine synthase	F: PF00849	ECOD (1.6)
E [auth C]	PF01479	e3dh3C2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Alpha-L RNA-binding motif	F: PF01479	ECOD (1.6)
E [auth C]	PF00849	e3dh3C1	A: a+b two layers	X: Alpha-beta plaits	H: Pseudouridine synthase (From Topology)	T: Pseudouridine synthase	F: PF00849	ECOD (1.6)
G [auth D]	PF01479	e3dh3D2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Alpha-L RNA-binding motif	F: PF01479	ECOD (1.6)
G [auth D]	PF00849	e3dh3D1	A: a+b two layers	X: Alpha-beta plaits	H: Pseudouridine synthase (From Topology)	T: Pseudouridine synthase	F: PF00849	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.290.10	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (4.3.0)
A	3.30.2350.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	Pseudouridine synthase	CATH (4.3.0)
C [auth B]	3.10.290.10	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (4.3.0)
C [auth B]	3.30.2350.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	Pseudouridine synthase	CATH (4.3.0)
E [auth C]	3.10.290.10	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (4.3.0)
E [auth C]	3.30.2350.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	Pseudouridine synthase	CATH (4.3.0)
G [auth D]	3.10.290.10	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region	Chain A	CATH (4.3.0)
G [auth D]	3.30.2350.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	Pseudouridine synthase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B], E [auth C], G [auth D]	PF00849	RNA pseudouridylate synthase (PseudoU_synth_2)	RNA pseudouridylate synthase	-	Family
A, C [auth B], E [auth C], G [auth D]	PF01479	S4 domain (S4)	S4 domain	The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...	The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B], E [auth C], G [auth D]	Ribosomal large subunit pseudouridine synthase F	isomerase activity pseudouridine synthase activity catalytic activity intramolecular transferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid rRNA pseudouridine synthase activity tRNA pseudouridine synthase activity catalytic activity, acting on a tRNA RNA binding binding organic cyclic compound binding nucleic acid binding	ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process rRNA processing enzyme-directed rRNA pseudouridine synthesis rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis ribosome biogenesis organic substance metabolic process organic substance biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process ribonucleoprotein complex biogenesis cellular biosynthetic process RNA metabolic process rRNA processing enzyme-directed rRNA pseudouridine synthesis rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis ribosome biogenesis organic substance metabolic process organic substance biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process pseudouridine synthesis rRNA pseudouridine synthesis cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process RNA modification biosynthetic process macromolecule modification ncRNA metabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process tRNA processing tRNA pseudouridine synthesis tRNA modification tRNA metabolic process	-
B [auth E], D [auth F], F [auth G], H	stem loop fragment of E. Coli 23S RNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B], E [auth C], G [auth D]	IPR020103	Pseudouridine synthase, catalytic domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR002942	RNA-binding S4 domain	Domain
A, C [auth B], E [auth C], G [auth D]	IPR020094	Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR000748	Pseudouridine synthase, RsuA/RluB/E/F	Family
A, C [auth B], E [auth C], G [auth D]	IPR036986	RNA-binding S4 domain superfamily	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR006145	Pseudouridine synthase, RsuA/RluA-like	Domain
A, C [auth B], E [auth C], G [auth D]	IPR018496	Pseudouridine synthase, RsuA/RluB/E/F, conserved site	Conserved Site
A, C [auth B], E [auth C], G [auth D]	IPR042092	Pseudouridine synthase, RsuA/RluB/E/F, catalytic domain	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.